(The H4-Index of Microbiome is 69. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-10-01 to 2023-10-01.)
Microbiome definition re-visited: old concepts and new challenges690
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank464
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences373
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses330
Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons227
Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization222
Review: microbial transformations of human bile acids204
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes198
Gut microbiota and cardiovascular disease: opportunities and challenges187
RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs178
Suppressed N fixation and diazotrophs after four decades of fertilization175
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling173
Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis171
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity169
Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study169
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens154
Specialized metabolic functions of keystone taxa sustain soil microbiome stability153
Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir152
Advancing functional and translational microbiome research using meta-omics approaches142
Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression142
Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories139
Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance133
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition131
Disentangling the mechanisms shaping the surface ocean microbiota130
Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision?125
Rhizosphere protists are key determinants of plant health116
Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients113
Using soil bacterial communities to predict physico-chemical variables and soil quality113
Lung function and microbiota diversity in cystic fibrosis109
Plant developmental stage drives the differentiation in ecological role of the maize microbiome109
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2108
β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice106
Disease-induced changes in plant microbiome assembly and functional adaptation106
Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes103
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks101
Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-br100
Ochratoxin A induces liver inflammation: involvement of intestinal microbiota100
Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome97
Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste96
Viruses in the Built Environment (VIBE) meeting report94
Metagenomic analysis reveals the microbiome and resistome in migratory birds93
Rhizosphere community selection reveals bacteria associated with reduced root disease90
Gut microbiome composition differences among breeds impact feed efficiency in swine89
Gut microbiota-derived indole 3-propionic acid protects against radiation toxicity via retaining acyl-CoA-binding protein89
Predictable modulation of cancer treatment outcomes by the gut microbiota87
Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants86
Microbiome of vineyard soils is shaped by geography and management85
Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation82
Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota81
From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators81
Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia80
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants80
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula79
Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed77
Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice77
The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment76
Thousands of previously unknown phages discovered in whole-community human gut metagenomes76
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics75
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas75
Challenges in exploring and manipulating the human skin microbiome74
Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem74
Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis73
Direct impact of commonly used dietary emulsifiers on human gut microbiota72
Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration71
Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate71
Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain71
Host habitat is the major determinant of the gut microbiome of fish70
Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease70
A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community69
It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome69